In 2011, Noah Phiri was working with local farmers in Kenya to combat the fungal pathogen that causes coffee leaf rust when another virulent plant disease began wiping out maize in the country’s southwest corner. Infected plants developed pale streaks on their leaves, then wilted and died. Some farmers lost as much as 90 percent of their crop that year. Phiri, a plant pathologist at the U.K.-based Centre for Agriculture and Biosciences International (CABI), raced to identify the culprit. He and his colleagues collected samples of sick plants and sent them off to the plant clinic at the Food and Environment Research Agency (now Fera Science) in York, U.K. There, researchers sequenced RNA molecules expressed in the infected corn and identified two viruses that were at the root of the epidemic.

Guatemala has declared a state of agricultural emergency after coffee rust fungus has affected approximately 193,000ha of coffee, equating to 70% of the national crop. As a result of the outbreak, Guatemala is releasing $13.7m (£8.7m) in emergency aid to help farmers buy pesticides and to inform farmers on ways to manage the disease. Honduras and Costa Rica have already declared national emergency and El Salvador and Panama are also affected.

Coffee is a major export crop in many Central American countries and it is thought that this disease outbreak, which has been called “the worst seen in Central America and Mexico” by John Vandermeer, ecologist at the University of Michigan, will lead to big job losses. The Institute of Coffee in Costa Rica has estimated that the latest coffee rust outbreak may reduce the 2013-2014 harvest by 50% or more in the worst affected areas.

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